11-89710305-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146162.1(TRIM77):āc.7T>Gā(p.Ser3Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000653 in 1,516,638 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001146162.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM77 | NM_001146162.1 | c.7T>G | p.Ser3Ala | missense_variant | 1/6 | ENST00000398290.7 | |
TRIM77 | NM_001271942.1 | c.7T>G | p.Ser3Ala | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM77 | ENST00000398290.7 | c.7T>G | p.Ser3Ala | missense_variant | 1/6 | 5 | NM_001146162.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000793 AC: 12AN: 151400Hom.: 0 AF XY: 0.000113 AC XY: 9AN XY: 79440
GnomAD4 exome AF: 0.0000616 AC: 84AN: 1364324Hom.: 1 Cov.: 33 AF XY: 0.0000556 AC XY: 37AN XY: 665678
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.7T>G (p.S3A) alteration is located in exon 1 (coding exon 1) of the TRIM77 gene. This alteration results from a T to G substitution at nucleotide position 7, causing the serine (S) at amino acid position 3 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at